Kabuto brings Yukimaru to a lake, subjecting the boy to a state of pain with pills and a chakra amplifying helmet in an attempt to draw out a mysterious creature. Guren branches off from her men to meet up with Orochimaru while he had Sasuke fight an army of 1000 Sound Ninja as training. Sasuke defeats them all, sparing his beaten opponents as he wants to kill only Itachi. At the hot spring village, Naruto has enough of working with Gamariki, so uses the Summoning Jutsu to continue his training with Gamakichi and Gamatatsu, despite still not understanding the concept of connecting to another person's heart. Kabuto and Yukimaru arrive at the Hot Springs Village where Naruto and Jiraiya are, with Naruto encountering Yukimaru. Meanwhile, Orochimaru assigns Guren a special mission, and tempts her with the possibility that he will allow her to be his next vessel instead of Sasuke.

More than ten years ago, the rule of the Five Great Shinobi Nations was destabilized, throwing the world into a conflict later to be known as the Third Great Ninja War. The future Fourth Hokage Minato Namikaze assigns young Kakashi, Obito of the Uchiha clan, and Rin, a medical ninja, on a mission to Kannabi Bridge...

Under Kakashi's command, the Leaf ninja set off to find Itachi. Using Kakashi's ninja hounds, they gather as much information as they can on Itachi. Meanwhile, the members of the Hebi also scatter to look for information on Itachi. Led by the ninja hound tracking Sasuke's scent, Sakura arrives in town and draws near to Karin.

Sasuke asks where Itachi is and slices through Tobi, as Deidara retreats to a distance. Tobi gets back up unharmed as Deidara retaliates with his chakra-level 1 (C1) explosives. Sasuke escapes with a simple substitution jutsu forcing Deidara to use one of his C2 creations, the C2 Dragon. Working with Tobi, they forced Sasuke to use the Curse Mark. In the end, Sasuke defeats their combos, and Deidara is left with no choice but to use his trump card that was meant for Itachi, the C4 Karura.

As Deidara's C4 Karura detonates, Sasuke perishes. Believing to have won, Deidara drops his guard, only to be pierced by Sasuke's Chidori. Deidara uses a clay clone and attacks Sasuke again, but Sasuke is able to break out of the C4 Karura. After being asked how he had survived, Sasuke reveals that he was never harmed and that Deidara was under his genjutsu, and that he noticed Deidara used Earth Style hand signs to mould his detonating clay, which was inferior to Sasuke’s Lightning Style Chidori. Deidara recalls how we was defeated by Itachi and recruited to the Akatsuki as a result of Itachi’s Sharingan, giving him a hatred for such eyes. Deidara tries to kill Sasuke but is misled by his Sharingan again. Both combatants collapse and Sasuke deactivates his Sharingan. Angered at being mocked, Deidara unveils his final attack, an explosion of art, where he turns himself into a living bomb and detonates himself in an attempt to kill Sasuke.

Upon noticing the blast, Suigetsu summons Manda and finds out that Sasuke had used him, alongside a transportation jutsu, to escape. Unable to survive, Manda dies from his wounds. Meanwhile, Zetsu informs the remaining Akatsuki of the deaths of Deidara, Tobi, and Sasuke during their battle. After the meeting, Itachi tells Kisame that Sasuke is not dead. Naruto and the others get to the crater caused by Deidara’s explosion, and using Kiba's tracking skills they begin to track down Sasuke's scent to where he is resting with his team. Meanwhile, the Akatsuki leader is revealed to be Pain. He and his partner, Konan, are then ordered to capture the Nine-Tailed Jinchūriki by a mysterious man, Tobi, who claims to wield the true power of the Sharingan, and reveals his identity to be Madara Uchiha.

Jiraiya arrives in Konohagakure and tells Tsunade that he has information regarding Pain's location. In the meantime, Karin senses that they're being followed by the Hidden Leaf Shinobi and asks Jugo to help her throw off their pursuers. As Hebi departs, Naruto encounters Itachi and tells him he sees Sasuke as a sworn brother. After talking, Itachi departs, having more pressing matters to attend to. Meanwhile, Jiraiya and Tsunade share a drink, and discuss how the Akatsuki leader is based in the insular Hidden Rain Village, currently embroiled in a civil war with Pain leading one of the sides, and how the village has been the battleground for larger surrounding lands. Jiraiya reminisces about his former student and Naruto's father, Minato Namikaze and how he quickly rose to become the Fourth Hokage. Speaking of future Hokage candidates, Tsunade likens Naruto to his mother, Kushina Uzumaki. Jiraiya warns Tsunade about the Foundation before Jiraiya departs for the Hidden Rain Village, to confirm Pain’s location in a life-threatening mission.

Back in the times of the Third Hokage's youth, the young, soon-to-be Sannin are assigned to Hiruzen Sarutobi's platoon. Being fascinated by Sarutobi’s summoning jutsu, Jiraiya tries it himself, only to teleport himself to Mount Myoboku. There, Jiraiya trains under Fukusaku and meets the Great Lord Elder who has a vision of his future. Afterwards, Jiraiya goes on a journey with the goal of fulfilling his destiny, meeting many strange characters on the way.

Due to the Second Great Ninja War, Jiraiya, Tsunade and Orochimaru are sent to the Hidden Rain Village, where they are named the "Legendary Sannin" by Hanzo of the Great Salamander. While in the village, Jiraiya meets with Yahiko, Nagato and Konan who request help from him. Jiraiya accepts and proceeds to train them before returning home. He is later informed that all three children were killed. Some time later, Jiraiya trains Minato, who together with Kushina, names their unborn son "Naruto" after the main character in Jiraiya's first book.

Jiraiya successfully infiltrates the Village Hidden in the Rain, where he wanders around town and speaks to the inhabitants about their leader, Pain. Unsuccessful in gathering information, he captures two lower ninja of the city in a frog's stomach, who ends up telling him that the mysterious Pain had defeated the former leader of Rain, Hanzo, whom the Sannin together couldn't defeat. Meanwhile, Pain orders Konan to search for the intruder and she folds herself into origami butterflies.

Jiraiya summons Gerotora and talks with it about how he's going on a battle and to be ready. He also says that the Nine-tails attack was not a natural disaster, it was summoned by someone. Jiraiya revealed that it was summoned by an Uchiha and it was Madara Uchiha. Pain changes into a new body and tells Konan to confront Jiraiya, their former sensei. Pain soon arrives himself and discusses his personal ideology and the Akatsuki's goals with Jiraiya. He reveals that the collection of the Tailed Beasts is in order to create a Forbidden Jutsu weapon that will be able to destroy entire nations in an instant, so that the world will be able to "mature" and develop an aversion for war. Pain then summons a crab to attack Jiraiya, which is defeated before Jiraiya summons a giant frog named Gamaken.

Jiraiya and Gamaken begin their battle against Pain, who has hidden himself using camouflage. Jiraiya uses a barrier jutsu to try and find him while preparing to enter Sage Mode. Meanwhile, Pain assaults Jiraiya with a barrage of animal summons, such as a multiplying dog, a rhino, a bird and a bull, and Jiraiya finally enters in Sage Mode, after sending Gamaken back home. He summons Lord Fukasaku and Lady Shima, who find Pain and destroy his chameleon. Pain then summons two more bodies.

Jiraiya blinds one of the new Pains, and Lord Fukasaku suspects that all three share the same eyes and vision, while Jiraiya realizes that each of the bodies has only one specific purpose. Jiraiya stalls for time while Lord Fukasaku and Lady Shima prepare a powerful genjutsu to defeat the bodies and are successful in doing so. As Jiraiya leaves, another Pain ambushes Jiraiya destroying his left arm. As Jiraiya looks up he sees six Pains, including the three that were killed. He stands horrified wondering just who and what Pain is.

Jiraiya goes into deep panic thinking Pain is either Yahiko or Nagato, as Pain possesses Rinnegan which Nagato had and he appears as Yahiko. Jiraiya kills one of the Pains only to realize he's fought him before. Lady Shima leaves on Jiraiya's request before Jiraiya realizes that he has met all of the Pains before. Jiraiya figures out who Pain is but it is unable to relay the message as Pain's attack crushes Jiraiya's throat. As he begins to die, he remembers Naruto's determination and forces himself awake, where he writes a message on Lord Fukasaku's back. Pain then blasts him into the ocean, where Jiraiya dies happy, sure that Naruto is the Child of Prophecy.

While Naruto's team continues their search for Sasuke, Sasuke meets Itachi in a cave, fights an illusion, and is told to come to the Uchiha hideout. On their way, Sasuke's team is intercepted by a shadow clone of Naruto, which Sasuke easily dispatches. The real Naruto quickly sends his team after Sasuke, but they are stopped by Tobi. Meanwhile, Team Hebi is confronted by Kisame who won't let anyone but Sasuke pass. Sasuke carries on while his team, specifically Suigetsu, faces Kisame.

As Sasuke approaches the Uchiha hideout, Itachi recalls his past with his little brother and the assassination that he carried out after joining the Anbu and being under close watch for his suspicious activities. When Sasuke arrives, he declares that his eyes have shown him Itachi's death and the fated battle between the two brothers begins. Itachi's illusions deceive Sasuke as he explains that he conspired with Madara Uchiha, the Leaf's founder and the first to awaken the Mangekyo Sharingan, when he killed their clan.

As Zetsu watches on, Itachi explains to Sasuke the real secret behind the Mangekyo Sharingan, and the history of the Uchiha clan. Besides being able to tame the Nine-Tailed Fox, the Mangekyo will eventually rob the user of his eyesight and the only way to overcome this obstacle is to steal the Sharingan eyes of that person's sibling. Sasuke retaliates against Itachi's assaults, but he is eventually pinned to a wall and has one of his eyes seemingly stolen by Itachi.

As Itachi moves in to take his remaining eye, Sasuke manages to overcome the Tsukuyomi he was placed under. With Genjutsu now useless, the brothers switch to Ninjutsu, with Sasuke gaining the upper hand. Itachi then unleashes Amaterasu, however, Sasuke uses a Substitution Jutsu to escape the flames. Itachi berates Sasuke, claiming he now has no chakra left, but Sasuke reveals that he had come prepared, and has one last technique left that would make his dream of killing Itachi a reality.

Sasuke summons his ultimate Lightning Jutsu, Kirin, and directs it at Itachi. However, Itachi rises again and reveals his final Mangekyo technique, Susano'o. With Sasuke weakened, Orochimaru is able to break free from his restrictive chakra and attempts to take Sasuke's body. However, Itachi retaliates by sealing him away into another dimension, ridding Sasuke from the Cursed Seal of Heaven and the own Orochimaru. Out of jutsu, Sasuke is left at Itachi's mercy, but at the last second, Itachi taps Sasuke on his forehead and collapses onto the ground, dead.

The Leaf Ninja continue to fight Tobi, but all of their attacks manage to phase right through him. Shino manages to trap Tobi with a beetle sphere but Tobi uses a teleportation jutsu in order to escape. Zetsu arrives to inform Tobi the outcome of the Uchiha match, the Leaf Ninja overhears, and Madara drops his goofy persona in order to leave the fight; revealing his Sharingan, and to collect the brothers' bodies. Sasuke wakes up in a cave and Madara approaches him, introducing himself. An Amaterasu is unleashed from Sasuke's left eye turned Itachi's Mangekyo Sharingan, but Madara recovers from it and mentions how in-depth Itachi's plans were. Sasuke asks what he means, and Madara tells him the truth that Itachi was trying to protect him.

Madara tells Sasuke about the real history of the Uchiha and how they and their rivals, the Senju clan, led by the future First Hokage, Hashirama Senju, once made a pact to unite the two clans as one and to make the first hidden village, Konoha. Afterwards, the Senju spied on and secretly discriminated against the Uchiha, forcing Madara, their leader, to leave and try to exact revenge upon them. Years later, the Uchiha were planning a coup d'etat on the village and Itachi was chosen by the village leaders to spy on the clan from the inside.

Madara continues the by informing the truth about Itachi to Sasuke that Itachi was a double-agent who was assigned to leak intel on the Uchiha back to the village. He then contacted Madara to help him undertake his mission of exterminating the Uchiha clan. They succeeded in their mission, although Itachi couldn't bring himself to kill Sasuke. Some time later, Sasuke reminisces on Itachi's final words to him, before breaking down into tears. Heartbroken and vengeful, he changes his team's name to Taka and declares that their goal is to destroy Konoha, revealing his newly awakened Mangekyo Sharingan.

The Konoha teams decide to head back home as Sasuke remembers that he saw Itachi crying after the massacre. He then states that he cannot rebuild the Uchiha clan in the same way that Itachi had envisioned. Madara, happy that he can use Sasuke for himself, assigns Taka the task of capturing the Eight-Tails while Akatsuki hunts the last two. Taka tracks down the host, Killer Bee, to the Land of Lightning and engages him in battle. Bee manages to overpower Jugo and Suigetsu before Sasuke steps up to fight him one-on-one.

Sasuke fights Killer Bee and is injured by his swords. Karin heals him, and Sasuke, Suigetsu, and Jugo then begin a combined assault on Bee until he decides to use the Eight-Tails' power. Sasuke is injured and revived again by Jugo, who regresses in age as a result. All healed, Sasuke unleashes Amaterasu on Bee in desperation, finally able to subdue him. Meanwhile, two Cloud ninja watch the fight from a cliff, and they notice the Uchiha crest on Sasuke's back. They rush the news to Bee's big brother, the Fourth Raikage Ay.

On a cliff a young man, a girl, and her servant are attacked by a group of ninja. The servant sends word to the Hidden Leaf Village for aid and the young man, Utakata, leaves with the girl, Hotaru. Back in the Leaf, Tsunade tells Shizune of a clan named the Tsuchigumo and an elder named En no Gyoja who developed a forbidden jutsu, which the Leaf are to prevent the theft of. Team 7 and Yamato arrive to assist Utakata and Hotaru, but Utakata leaves immediately with faith that they will assist her.

The ninja bandits have a meeting with their leader about the Forbidden Jutsu. Elsewhere Team 7 tricks Hotaru into staying as her bodyguards until they reach her village. After reminiscing about the past, Utakata wakes up to come across the ninja bandits and fights them until he is cornered by their barrier jutsu which soon explodes. Team 7 finally reach Hotaru's village and they leave her in their care, but Naruto Uzumaki senses something troubling and heads back to the village, suspicious of the villagers' attitude toward Hotaru.

Hotaru's uncle shows her to her room, where she is ambushed by the bandits. They are trapped and Hotaru escapes into the forest, but the bandits catch up to her. Utakata saves her, and the bandit's leader shows that Utakata is being hunted for 50 million ryo. Utakata and Hotaru land in a secluded place where Hotaru shows him something on her body. Suddenly Mist Tracker Ninja attack Utakata and take Hotaru hostage. They tell Hotaru that Utakata killed his former master. Naruto soon arrives with Yamato and Sai.

The Hidden Mist ANBU and Yamato negotiate and it is hinted that Utakata is a Jinchuriki. It is then decided that Utakata will travel with the Hidden Leaf until their mission is complete before the Mist ANBU take him back to their village. Utakata didn't mean to kill his master; it is realized that while trying to separate the tailed beast from him, it came out and killed Utakata's master. Later Hotaru is hurt leading Naruto to find out that the Forbidden Jutsu is engraved into her back.

The bandits' leader appears on Mt. Katsurugi and listens in on a conversation between Tonbei, Hotaru, Utakata, and Team 7. Tonbei suggests that they should remove the Forbidden Jutsu from Hotaru for her safety, but Hotaru suggests searching for Shiranami, another person who could use the jutsu. Naruto leaves to go search for him and it is revealed that the bandit leader is Shiranami. Utakata leaves to speak with Tsurugi, but Tsurugi and the rest of the Anbu encounter a dog with Rinnegan eyes.

Naruto arrives at Shiranami's cabin and is captured by the bandits. Utakata, who had found a note left by Hotaru and was looking for her, arrives and drives the bandits away with his Six-Tails's chakra. Hotaru encounters Shiranami, who captures her and takes her to the Tsuchigumo village. He takes control of her and the villagers and takes her with him to unseal the Forbidden Jutsu. Naruto and Utakata track Shiranami and Hotaru to the village, but are attacked by the villagers and the bandits, who stall them until Team 7 arrives.

Shiranami has Hotaru in a binding jutsu that keeps her restrained in one place. Shiranami asserts that Hotaru is nothing but a vessel to collect the natural chakra energy that will release the jutsu. Utakata and Naruto arrive but are held back by Shiranami's binding jutsu. However, they manage to free themselves. Meanwhile, Team 7 struggles with the bandits and villagers and is unable to advance. Finally, Shiranami gathers all the energy he requires and releases the Fury Jutsu.

Hotaru cries, believing that she killed Naruto and Utakata, however they still manage to move. Meanwhile, Team 7 fights the bandits and defeat them. Hotaru's body starts to overflow with natural chakra and Shiranami tries to escape but is defeated by Naruto. Utakata then uses his Six-Tails’s chakra to consume and stops the flow of chakra. In the end, Team 7 leaves and Hotaru and Utakata start their travels, but Utakata is ambushed by Pain and defeated, using his last strength to blow bubbles to tell Hotaru to live on.

After extracting the Six Tails from Utakata, the Akatsuki note that only two Jinchuriki remain to be captured as Sasuke Uchiha hands the unconscious Killer Bee over to Tobi. Meanwhile, the Fourth Raikage Ay learns of Taka's action and is livid that they stole his brother. At the Hidden Leaf Village, after recalling his encounter with Itachi prior to his battle with Sasuke, Naruto Uzumaki is shell-shocked by a terrible imformed from Tsunade and Fukasaku that Jiraiya is killed by Pain.

Naruto, complety heart-broken about learning Jiraiya's death by Pain, walks off and recalls his time with his mentor. Fukasaku shows Jiraiya's chakra-encrypted code to Tsunade who has Shikamaru give to their village's best code breaker in translation. The next day, told that the cipher might be known by something Jiraiya knows, Shikamaru visits Naruto and gives him some peace of mind by revealing that Kurenai is pregnant with Asuma's child and that they should stop being children and become the best of what their mentors saw in them.

The scientists inspect the body of Pain's Animal Path, while Naruto and Shikamaru identify the message. Naruto, noticing the number nine emulated for the "Ta" katakana on the "Make-Out Tactics" Book, informs Tsunade and Fukasaku that the number code unveils the sentence saying, "The real one is not there". Naruto vows to avenge his master's death and Fukasaku memorizing Jiraiya's actions decides to take Naruto to Mount Myoboku for training in Sage Mode. There, meeting Gamakichi who tries to help him understand Fukasaku's lecture, Naruto learns the basics of Sage Jutsu and the risk of death.

After intense training, Naruto successfully gathers energy to master Sage Mode for the first time and surpass Jiraiya. Fukasaku teaches Naruto with Frog Kumite, a senjutsu-enhanced taijutsu that increases the range for physical attacks. Meanwhile, the Raikage A orders Samui, Karui and Omoi to find Bee and deliver the letter for Tsunade about capturing Sasuke.

While Naruto finishes training on Mount Myoboku, Pain invades the Hidden Leaf with his new Animal Path Pain. While Inoichi reads the Animal Path's mind and Shizune leads a biopsy team to find secrets behind the metal piercings for the Leaf's Intel Division, Pain interrogates the villagers. Knowing that Pain is attacking the village, Tsunade orders them to get Naruto back.

Danzo, Homura, and Koharu ask Tsunade to cancel Naruto's return, but she convinces them to let Naruto come for Pain and Konan. As Tsunade protecting them failed, Danzo kills the messenger frog from getting to Naruto. Kakashi Hatake meets to confront Pain, allowing Iruka's escape.

Kakashi is stopped by Pain's Asura Path from helping Choza as he and Choji are outmatched against Pain. While Pain annihilates Choza's squad as his Asura Path attacks Kakashi, Choji escapes and get to Tsunade.

Naruto attempts to merge with Fukasaku, so that he can move in Sage Mode while Fukasaku gathers Nature Energy for him. But the Nine-Tails forces them to find an alternate method for Naruto to enter Sage Mode in battle. As the Interrogation Corp fights off Pain's new Animal Path and barrages them with an assortments of animal summonings, Ibiki fails to stop them.

Pain's Naraka Path displays its mysterious power against two leaf shinobi while Konohamaru Sarutobi watches in horror. Pain senses Konohamaru's presence but is interrupted by Ebisu who takes on Pain in order to allow Konohamaru to escape. After seeing Ebisu about to be killed, Konohamaru intervenes and after learning of Naraka's ability, judging souls and then reaping the sinner of their life, with a Shadow Clone, he unleashes the Rasengan and is able to keep Naraka at bay.

As the Inuzuka and Aburame clans battle with his Preta Path and Konan respectively, Pain meets with Tsunade, who recognizes him as Yahiko. As Naruto learns of the village's situation, Human Path discovers his location and then kills Shizune, transmitting the intel to Pain who uses his gravity-manipulating Deva Path ability to completely destroy the village in frustration with Tsunade. In the newly formed crater in the heart of Konoha, Naruto appears in Sage Mode with a small armada of toads following Sakura Haruno's cries for his return.

Naruto confronts Pain as his other Five Paths reappear. Asura Path attacks Tsunade and Naruto destroys it, telling Tsunade to leave. She does so and reverts to her old self with Sakura. Naruto charges forward as the toads deal with Animal Path's summons. Naruto fights Preta Path with Frog Kumite and defeats it before speaking to Pain. He reveals that they were both Jiraiya's apprentices and how he only wants peace. Angered with his hypocrisy, Naruto throws a finally completed Rasen-Shuriken at the remaining Paths of Pain.

Naruto successfully begins taking out Pain's bodies one after another, but when his Sage Mode reaches its limit, Pain attempts to take control of the battle. Naruto throws another Rasen-Shuriken but it's absorbed by a revived Preta Path. But Fusaku reveals that Naruto created two clones that are harvesting Natural Energy for him, Naruto summoned one of the clones to disperse and obtained the energy to resume Sage Mode. Naruto manages to kill the Naraka Path, just to get repelled by a recovered Pain who uses another Shinra Tensei on the toads. Naruto realizes he can't use taijutsu or ninjutsu on the remaining paths, so he will have to fight them using a genjutsu suggested by Fukasaku.

As Hinata worries about Naruto, Inoichi and the others try to find the real Pain. Naruto continues to fight back the remaining paths but is captured by Preta Path. It absorbs his Sage Mode chakra and is petrified due to the uncontrollable Nature Energy. Fukasaku then attempts to trap Pain in a Genjutsu, but is killed. Pain then impales several Chakra receivers into Naruto's body, immobilizing him to be manipulated by Nagato. Pain explains that the world peace Jiraiya envisioned can not be achieved due to hatred among the people, revealing his intent to use the tailed beasts' power to have every living know suffering and fear it. As he has Pain ask Naruto if he could think of another path to peace, Nagato states that his ideal peace is almost in fruition.

Hinata decides to come to Naruto's aid as he was about to be manipulated by Nagato's Chakra receivers, finally admitting her love for Naruto as she fights a losing battle against Pain. But despite knowing she may likely die, Hinata remains adamant before she is quickly defeated, stabbed by Pain, and is seemingly unconscious. As Pain explains that the hate from losing loved ones is why there can never be peace in the current world, Naruto goes berserk as the Nine-Tails chakra begins to surface. Meanwhile, Konoha ninja start the search for Nagato.

Naruto enters his Four-Tailed Fox form and attacks Pain, who manages to repel his attacks. Angered even further when Pain mentions Sasuke, Naruto continues his transformation into a Six-Tailed Fox form to gain advantage. Pain decides to fall back from the village toward where Nagato is to trap Naruto with Planetary Devastation, a powerful jutsu that the Sage of Six Paths used to create the moon, to trap the Nine-Tails Jinchuriki within a miniature moon in midair. But Naruto starts breaking free to Pain's big shock, now in a monstrous Eight-Tailed Fox form, he launches a powerful wind roar against Pain sending to a rock and injuring him. Within his mind, Naruto succumbs to the Nine-Tails telling him to embrace his hate and destroy everything. Naruto was about to remove the seal to completely release the Nine-Tails when he was stopped by the Fourth Hokage Minato Namikaze.

Minato appears within Naruto's psyche, revealing himself to a chakra imprint of the Fourth Hokage as he takes Naruto to another part of his mind to discuss things away from the furious Nine Tails. It was there that Minato revealed himself as Naruto's real father, making Naruto further conflicted on why his own father made him a jinchuriki. But Minato reveals he only sealed half of the Nine-Tails into Naruto, revealing that the Nine-Tails' attack on the Hidden Leaf Village 16 years ago was Tobi's doing, theorizing that Pain may be a pawn of the Akatsuki's mysterious masked man to Naruto's big shock. Placing his faith that Naruto will find the answer to Pain's question, Minato restores the Nine Tails seal before fading away. Back to normal, and no means to renew his Sage Mode, Naruto confronts Pain and demands to meet Nagato himself. Pain refuses, resulting in a fight with Naruto stabbing himself with a Chakra Receiver to pinpoint Nagato's location. After using up his final Rasen Shuriken followed by a mass clone attack to force his opponent to exhaust his gravity manipulation, Naruto uses the 5-second window to land a final Rasengan on Pain.

Naruto finally defeats Pain with his final Rasengan, removing his Chakra Receivers before heading to Nagato's location, having Katsuya tell the others not to follow as Sakura finishes healing Hinata. Naruto encounters Inoichi and Shikaku on the way, the latter honoring Naruto's request to stand down to Inoichi's dismay. Naruto finds Nagato and Konan, the former impaling him with a Chakra Rod to control him. But Naruto breaks free, stating his murderous intent as Konan gets between him and Nagato before the youth stops himself. Naruto states Jiraiya's belief for a peaceful world with Nagato asking if he can still believe in Jiraiya's "peace" after all that has happened. Noticing Nagato and Konan are not like the other Akatsuki members, Naruto requests to hear their real story before giving him his answer.

Three years before Pain's attack on the Hidden Leaf Village, Naruto trains in preparation for the Chūnin Exam's final rounds when he hears Jiraiya speak of “the Fourth Hokage's legacy". Using information from Guy, Naruto, Sakura and Team 10 head to the Honegami Grounds, where they are instructed by a disguised Guy to enter and complete the obstacle course and obtain the Secret Technique. Meanwhile, Hidden Rain Ninja begin their pursuit.

Learning that Naruto will answer his question after learning how he and Konan ended up as they are, Nagato recalls his two real moments of pain, the first of which being the night his Rinnegan activated upon seeing his parents accidentally killed by Leaf Ninja. He then tells Naruto about how he met Konan and Yahiko, all three of them having to resort to thievery to stay alive. After seeing Hanzo the Salamander battle the Three Sannin, they set out to find the three ninja so that they can be taught ninjutsu.

Nagato continues talking to Naruto and describes his second pain, how he and Konan helped Yahiko use what they learned from Jiraiya to create the Akatsuki to bring peace to Hidden Rain Village. But Hanzo deemed Yahiko's group a threat to his regime and allied with Danzo to kidnap Konan. Hanzo orders Nagato to kill Yahiko if he wants her to live and Yahiko sacrifices himself for Konan's sake, horrifying Nagato and forcing him into the crippled state and state of mind he is in today.

With Nagato's real story done, Naruto answers that he still cannot forgive him but will not abandon their sensei's legacy and will keep striving for peace no matter what pain he is put through. Nagato reflects on Naruto's words, thinking back to how inspired the lead character in Jiraiya's story who Naruto was named after. This causes Nagato to decide to put his faith in Naruto as he performs a technique that will sacrifice to revive all those that he killed in the Hidden Leaf with Konan considering the consequences of its use.

Nagato finishes reviving everyone he had killed and dies due to running out all of chakra. He entrusts his dreams to Naruto and Konan likewise decides to believe in him. After retrieving Nagato and Yahiko's bodies, she gives Naruto a bouquet of flowers symbolizing the hope Naruto represents. After erecting a memorial for Jiraiya, Naruto returns to the village and after years of pain and isolation, finally is heralded as the Hidden Leaf Village Hero.

Iruka has just become Naruto Uzumaki's Academy homeroom teacher. Another teacher advises Iruka to not mistreat his students so that they will not cause trouble. But Naruto still causes mischief, as he is pained by his teacher's words to his class bullies to leave him alone and just ignore him. Lastly, Naruto discovers that Sasuke Uchiha is the only survivor of the Uchiha clan.

Upset after being rejected by a group of students, Naruto dresses up as a spirit to scare them, only to be scolded by Iruka later. Naruto gets angry and claims he will never return to the Academy again, running away from a very confused Iruka. Afterward, Naruto is tricked into going into the forest to retrieve a souvenir from a recent battle by the kids he scared. In return, they falsely promise to accept him into their group, hoping Naruto will be killed by the enemy still lurking out there.

Naruto runs into three female ninja from the Hidden Waterfall Village that want information on the Leaf Village's border patrol that Naruto had discovered earlier on. The ninja chase after Naruto and encounter Iruka. Iruka tries to protect Naruto as best he can, but is rescued by Kakashi Hatake. Iruka reconciles with Naruto. Back in the present Leaf Village, Yamato is informed by Shikaku that Naruto had defeated Pain. An ANBU member then tells Shikaku that he is expected at a very important meeting.

Watching Naruto and Sakura Haruno help out in the effort to rebuild their home, Kakashi has a flashback of when Hiruzen briefed him that he would be assigned them and Sasuke, accompanying him to Naruto's apartment where they find the long-expired milk which the boy drank before meeting up with his classmates on their last day of Ninja Academy and team assignments. Kakashi observes Team 7 from the behind the scenes, from Naruto's attempt to get close to Sakura to being outmatched by Sasuke when he attempted to attack him for hurting Sakura's feelings. It then goes back to the present as Kakashi notes that taking down the now rogue ninja Sasuke is his task to bear.

Years ago, after Team 7 completed their first mission and bid good bye to Tazuna and his grandson Inari, Naruto runs back to pick up a ramen coupon he left behind with Sasuke chasing after him. Meanwhile, Inari finds the coupon and runs off to find Naruto before he runs into bullies as they are all captured by Gatō's subordinates who intend to renew their criminal empire once the ninja have left. The boys are able to escape from the hideout, but the kidnappers follow with Inari luring them away so the boys can reach the village. Luckily, Naruto and Sasuke find signs of the struggle and save Inari at the last second while Gatō's subordinates were all captured, though Inari lost the coupon during the chaos. In the present following Nagato's defeat, Naruto and Sakura see Tazuna and an older Inari as they and Inari's former bullies are aiding in the rebuilding the Hidden Leaf Village.

In a flashback of Naruto and Sakura's, Team 7 is on a mission to take an ostrich called Mr. Ostrich to his home. They arrive at a village where they see a swordsman named Tsukado who has a vendetta to carry on a man named Katazu who killed his distant relative Shikazo. Tsukado fails to defeat him so Naruto decides to teach him unusual revenge lessons. Katazu has then took his brother's identity and attracted Shikazo's pursuers while Kageki and his family went into hiding. Tsukado decides not to kill him and ends their years of fighting though Kanabun wants them to keep fighting. The swordsmen, Team 7 and Mr. Ostrich chase the Kanabun Gang out of town.

Having faked his abduction by Sasuke, Killer Bee bided his time before emerging from the lake and confiding to the Eight Tails his intent to see the outside world and learn Enka from a man named Kin. Meanwhile, as Kakashi tells Naruto to keep what they learned of the Uchiha Massacre to himself until they know for full details, Sasuke uses his Susanoo to destroy the pillars and cause a cave in. Leaving Suigestu and Jugo behind, the former getting free in the chaos while the latter absorbs a corpse to restore himself, Sasuke has Karin take him to the summit room and attempts to go after a fleeing Danzo who Ao is pursuing. But Mei decides to fight Sasuke, revealing her three Chakra Natures and two Kekkei Genkai while overwhelming the injured Sasuke. Before she can finish him off once trapping him in a room to be subjected to her corrosive mist, Sasuke is saved by the spore clones that White Zetsu secretly laced on the Kage and bodyguards. However, Sasuke finds himself at the receiving end of Onoki's Dust Style attack and appeared to had been atomized by the time Ay and Gaara arrive. But Sasuke is revealed to have been saved at the last moment by Tobi, the masked ninja introducing himself to the present Kage as Madara while asking them for a reprieve so he can explain his ultimate goal: Project Tsuki no Me.

After sending Sasuke and Karin to another plane for the former's wounds to be tended too, Tobi explains his intention to unite everyone as one. Revealing he used Nagato's Rinnegan eyes to translate Uchiha stone tablet kept in the Naka Shrine, Tobi tells the Kage how the Sage of the Six Paths was once the Jinchuriki of a primordial monster called the Ten-Tails: The original form of the nine Tailed Beasts. Tobi reveals that the Sage, fearing the Ten-Tails would resume its rampage after his death, sealed the monster's body in what became the moon while its extracted Chakra was divided and given life as the nine Tailed Beasts. Tobi then reveals the Akatsuki's purpose is to gather the Tailed Beasts so he can revive the Ten-Tails and become its jinchuriki as part of his plan to take over the world by casting an Infinite Tsukuyomi to subjugate everyone to his will, revealing Killer Bee's faked capture to Ay. When the Kage refuse to hand over Killer Bee and Naruto, Tobi openly declares the Fourth Great Ninja War on them before leaving. Noting that Danzo is finished once the everyone at the Hidden Leaf learned of his conduct, with Mifune offering his forces while Mei's bodyguard Chojuro provides some intel on Kisame, the Kage proceed to form the first Shinobi Alliance while agreeing that it would be in their best interests to find Bee and place him and Naruto somewhere secluded. Meanwhile, deciding to see for himself if Sasuke truly has taken a dark path, Naruto finds Sakura with Kiba, Lee and Sai as she needs to talk to him.

Sakura attempts to release Naruto from his promise to her in retrieving Sasuke by claiming to love him and has given up on their former teammate. But Naruto sees through the real lie as she leaves with Kiba, Lee and Sai to hunt down Sasuke. At the same time, as Mifune deemed him no longer a risk as Killer Bee is alive, Ay is elected leader of First Shinobi Alliance and leaves to find and discipline his brother while the other Kage proceed to meet up with their respective feudal lords to inform them of the change of events. Meanwhile, Killer Bee meets with Kin and proceeds to learn Enka when they are approached by Kisame and a fight soon breaks out. But Samehada begins draining Bee's chakra substantially and grows much larger while Kisame takes this time to formally introduce himself to Kin and Bee.

With Ao in pursuit, Fu acts on Danzo's orders to steal back the Byakugan by any means necessary. With a Mind Transfer trap that the Hidden Mist ninja falls for with his mind becoming trapped in a puppet, Fu possesses Ao's body and attempts suicide by decapitation when stabbing the Byakugan out is impossible. But Mei and Chojuro intervene and rescue Ao, with Fu forced to cancel the jutsu and return to his body. Meanwhile, in a display of his skill as the Tailless Tailed Beast, Kisame fuses with Samehada and traps Bee inside of a Water Dome. While Kisame overpowers Bee in his Jinchuriki state before returning to his usual form, he is about to slice Bee's legs off when Samehada intervenes, as it became become fond enough Bee's chakra to heal the Jinchuriki against its user's wishes. Ay arrives at that time and helps a fully healed Bee decapitate Kisame with a combo attack before proceeding to discipline his brother.

As Jugo and Suigetsu are caught by the samurai, Naruto is confronted by Sai's ink clone and learn about both his peers' agreement about Sasuke and that Sakura intends to personally kill him to free Naruto of the burden she placed on him. The Sand Siblings arrive at that time and inform Kakashi of the events of the Kage Summit, with Kakashi to relay the upcoming war to his village while Gaara tells Naruto that he must consider the harsh truth about Sasuke and consider what "friendship" means to him. Meanwhile, revealed to have met the man during the Uchiha Massacre, Tobi intercepts Danzo who has Fu and his other bodyguard Torune Aburame hold him off while he undoes the seal on his right arm. While Torune manages to inflict Tobi's right arm with his flesh-eating nano-insects, the masked ninja uses his Transportation Jutsu to remove Danzo's bodyguards from the field while ripping off what is revealed to be a prosthetic limb. Tobi then brings a fully healed Sasuke and Karin before Danzo, who finishes unsealing his arm at that point and reveals it to be covered in multiple Sharingan, intending to add the eyes of the two Uchiha to it.

Kakashi requests Sai's clone to take him to Sakura to stop her from fighting Sasuke, telling Yamato to take Naruto back to the village while sending his ninja hounds ahead of them with information about the Five Kage Summit. But Naruto collapses from a panic attack over the events of learning what Sasuke has become and the prospect of even his friends wanting to kill Sasuke. Meanwhile, furious that Danzo assumes that he learned the truth of the Uchiha massacre from Itachi while deeming him truly a traitor, Sasuke uses his Susanoo to crush Danzo to death. However, Danzo appears to have survived unscathed, and the two begin to battle. Even Amaterasu is ineffective, and Danzo keeps coming back up after what should be a killing blow, due to a mysterious jutsu that is neither a cloning jutsu nor a genjutsu. As Karin notices one of the Sharingan on Danzo's arm close after being fatally cut down, Sasuke inflicts Danzo with a genjutsu in Itachi's image.

Sasuke places Danzo under genjutsu to kill him from behind, only to fall victim to the activation of a paralyzing curse mark placed on him earlier in the fight with Danzo insulting Itachi's act of sparing Sasuke while preparing to finish him off. But Sasuke's memories of Itachi allow him to cancel the curse and evolve his Susanoo as the fight soon recommences, Danzo's arm revealed to had been infused with the cells of Hashirama Senju by Orochimaru to use the Sharingan. At that time, Tobi deduces that Danzo is using the Uchiha Clan's forbidden jutsu Izanagi, which alters enough of the user's reality to avert death. Karin realizes the price for the jutsu is sacrificing a Sharingan for each use, realizing the jutsu's connection to the eyes on Danzo's right arm each permanently closing within 60 seconds of activation. The fierce fight between Sasuke and Danzo soon becomes one of stamina and will, Sasuke revealing he knew of Danzo's trick and that the latter only has a few Sharingan left to continue Izanagi.

Sasuke and Danzo's fight comes to an end when they stabbed each other with their blades, Danzo learning too late that Sasuke used his genjutsu to trick the old man in assuming he still have one more Sharingan to sacrifice for an Izanagi. Karin proceeds to heal Sasuke's injuries as a gravely injured Danzo to forced to rip off his right arm as he lost control over Hashirama's cells, the old man forced to grab the girl once regaining use of Shisui's sharingan to use as a hostage. Unbothered by Karin's peril as she is now a useless burden to him, Sasuke shoots his Chidori through her to fatally wound Danzo with the old man attempting to flee before being intercepted by Tobi as the mask ninja intends to take Shisui's sharingan. Danzo, remembering the lesson he learned when the Second Hokage sacrificed himself, uses the last of his strength to activate a sealing jutsu to trap two Sharingan users within his corpse. In his final moments as Sasuke and Tobi escaped the jutsu's radius, Danzo recalls how he never caught up to Hiruzen while lamenting of not becoming a Hokage.

As her group draw near to Sasuke's location, Sakura was about to pelt her companions with sleeping gas when Sai stopped her as he figured out her plan while revealing his own intent to stop them. Sakura uses the ensuing battle as a distraction to knock them out before moving forward with her plan to kill Sasuke alone, reminiscing about her history with Sasuke and failure to recognize his transition into who he is now. Back on the bridge, once Danzo's sealing jutsu ended, Tobi takes the old man's corpse so he can extract Shisui's Sharingan while advising Sasuke to finish off Karin as she would mostly likely become detrimental to them both. An injured Karin, recalling first meeting Sasuke in the Forest of Death during the Chunin Exams, finds herself about to be killed by him when Sakura arrives. Sasuke stays his hand as Sakura claims to have abandoned the Leaf Village to be by his side

Naruto wakes up from dreaming of his fight against Sasuke, finding himself under Yamato's care while learning Kakashi is going after Sakura. With Yamato refusing to let him go after his teammates while told they are returning to the Hidden Leaf, Naruto goes back to bed and uses a Shadow Clone to cover his escape. During that time, Naruto reminisces his history with Sasuke in wanting to be acknowledged by his rival while failing to truly understand Sasuke's pain of losing everyone he loved until Jiraiya's death along with everyone convincing him that Sasuke is a lost cause. While using Sage Mode to track Kakashi, thinking back to Jiraiya's ideals of understanding others and Gaara advising him on what he should do as Sasuke's friend, Naruto believes seeing Sasuke will allow him to decide his next course of action.

As Kakashi finds Sai and others while heading towards her, Sakura finds herself being tested by Sasuke when he reveals his new ambition is to slaughter everyone in the Hidden Leaf Village and requests proof of her loyalty to him by killing Karin. Sakura attempts to carry out the deed when Karin indirectly reveals Sasuke is about to kill her. But Kakashi intervenes with a slight advantage as Sasuke begins to suffer the blindness from using the Mangekyō Sharingan. Sakura, spiriting Karin to safety to heal, attempts to attack Sasuke from behind with a poisoned kunai. But Sakura's last second hesitation enables the blind Sasuke to grab the weapon from her, the girl only saved from certain death when Naruto takes the stab meant for her.

Naruto confronts Sasuke and berates him for attacking their teammate, only for Sasuke scoffs that he is no longer a part of Team 7 while stating his goal destroying the Leaf Village as his way to absolve the Uchiha of all the wrongdoings that befell them. Kakashi realizes that the repeated hatred coursing through the Uchiha's history has made Sasuke what he is now. He resolves to take care of Sasuke on his own, Naruto deducing his intentions and uses his clones to restrain him while runs at Sasuke with his Rasengan as Sasuke runs at Naruto with his Chidori. The two clash in a manner similar to what occurred at the Final Valley, the two ending up in a metaphysical plain where Naruto reveals to Sasuke that, while he used to be alone, he and Iruka pulled him from the brink. He was hesitant to approach Sasuke because he was jealous of his superior abilities, but he bonded with him all the same.

A few flashbacks occur showing the friendships and competitions that Naruto and Sasuke had over the years before their metaphysical discussion comes to an end as Tobi and White Zetsu arrive. Reminding Sasuke of what he told him years ago that high-level shinobi can read each other through their fists, Naruto tells Sasuke that he is prepared to die in their final battle. This causes Sasuke to tell Naruto that he will never change and that he would eventually destroy the Hidden Leaf village, before being spirited away by Tobi. Naruto suddenly falls ill moments later from Sakura’s poisoned kunai, but she heals him by administering the antidote. Meanwhile, to prevent further risk of blindness, Sasuke decides have Itachi's eyes transplanted into him.

After Naruto is administered the antidote, and Yamato's brief appearance in berating Naruto for getting him in trouble with the innkeeper, he, Sakura, and Kakashi take Karin with them to return to their village while retrieving Sai, Kiba, and Lee who were still out from Sakura's sleep gas. It was then that they run into Anbu from the Foundation, confirming Danzo's death and leaving the organization's fate to the next Hokage which may be Kakashi. Ay and his escort return to the Hidden Cloud Village and hold a council with the Land of Lightning's feudal lord over the events of the Five Kage Summit, gaining their lord's approval while requesting that he meet with the other Feudal Lords. Meanwhile, acting on Tobi's plan to infiltrate the Hidden Cloud, it is revealed that Kisame had hidden himself within Samehada while the "Kisame" that Ay and Bee killed was actually a White Zetsu clone in disguise.

The Feudal Lords agree to formally ratify the Allied Shinobi Forces during a limited televised conference, sending their messengers to the ninja as the Gaara, Mei, and Onoki returned to their villages. Gaara proceeds to hold a meeting among the Hidden Sand Elders to explain what happened at the Five Kage summit and the threat that the Akatsuki now pose to the world, learning of Danzo's death through one of the ninja dogs that Kakashi is sending to the other villages out of good faith. But even as everyone prepares for battle, some of the ninja are reluctant of forming an alliance with their former enemies. At the Hidden Leaf Village, after Shikamaru informed Ino and Choji of what his father told him before they and Team Ebisu welcome home Naruto and the others. Naruto tells Shikamaru to gather all their friends so he can tell them of what occurred while promising to let Team Ebisu interview him later for their newsletter, Konohamaru realizing something is different about Naruto as the youth smiles seeing how much of the village had been rebuilt in his absence.

Once his friends have gathered, Naruto insists that they leave Sasuke to him while keeping them in the dark about what occurred to their annoyance. Guy challenges Kakashi again for another match with full knowledge it may be their last once Kakashi officially becomes the Sixth Hokage. While the elders, Shikaku, and Kakashi are attending the conference to appointing the Hokage, Tsunade regains consciousness and is reinstated as the Fifth Hokage.

Gerotora seeks the Great Elder's advice over Jiraya's request to be stored inside of Naruto, the Great Elder requesting Naruto's presence to determine if it is the right course. Meanwhile as a fully recovered Tsunade calls a meeting to prepare for war against the Akatsuki, Naruto manages to elude Konohamaru and his friends to eat at a reopened Ichiraku. But before Naruto can eat free ramen, he is Reverse-Summoned to Mt. Myoboku by Fukasaku and brought before the Elder. Naruto learns that he will meet an octopus and face a youth with powerful eyes, recognizing the latter as Sasuke. When the elder approves of Naruto's answer, he gives Gerotora permission to request the youth to sign the scroll that is the key to consciously manipulate the seal on the Nine Tails.

With Naruto hesitant to sign Gerotora's scroll, the toad explains to Fukasaku that Naruto must be mentally able to extract the Nine Tails's chakra while separating it from the monster's will. Naruto, remembering the previous times that Nine Tails took over his body, signs the scroll in hopes to master it so he can fight Sasuke as an equal. After Gerotora forced himself down Naruto's throat, the youth is instructed by the Great Elder that he will meet the octopus from his prophecy on an isolated island. Meanwhile, after fully mastering his new abilities since absorbing Orochimaru's remains into himself, Kabuto Yakushi appears before Tobi while summoning the Reanimated corpses of Itachi, Sasori, Deidara, Kakuzu, and Nagato. Kabuto offers the surprised Tobi an alliance between them, offering his army of Reanimated ninja for Tobi's use in exchange for Sasuke. While Tobi initially refuses, he accepts upon seeing the figure within a sixth casket that Kabuto summoned. But Kabuto also deliberately lured the pursuit group under Anko to the Akatsuki's base.

Naruto, accompanied by Yamato, Might Guy, Aoba, and three other ninja, embarks on what he was told to be a "top-secret, S-rank mission". When the group reaches the only port in the Land of Fire, they find that the bay for over fifteen years is being terrorized by a giant marlin summoned from the Third Great Ninja War who can not return to its point of origin. With Yamato providing a boat and fishing rod, Naruto and his group set out to help a fisherman named Yusuke in catching the marlin to avenge his father. Following an epic fishing struggle, Yusuke finally catches the marlin with Naruto removing the embedded shuriken on the fish's forehead so it can return to its home. Naruto and the others finally set sail for the Hidden Cloud.

When Naruto Uzumaki's group reach Paradise Island, they are saved from a giant squid by the octopus from the Great Frog Sage's prophecy: Killer Bee in Eight-Tails form. Despite Naruto's initial reservations, he learns from the island's caretaker Motoi that Bee is a Jinchuriki who tamed his tailed beast and requests his mentorship. But Bee refuses, even more so when Naruto accidentally insulted him during a rap session after a fist bump. While Motoi takes offense to Naruto insulting Bee while coming to him for help, he takes him and Yamato to the Waterfall of Truth where Bee mediated as part of his training. Naruto learns that he must overcome the embodiment of his inner darkness before he can face the Nine-Tails.

While answering Naruto's need to learn more about Bee to find a way to overcome his dark side, Motoi confesses that he was Bee's childhood friend and he tried to kill him after he became the Eight-Tails jinchuriki since his father died when the tailed beast was sealed after being extracted from its previous host. While disguised at the time, Motoi continues to follow Bee and witnesses him overcoming his abuse by their fellow villagers. Later, as Naruto thinks about how to overcome his dark self, Motoi is grabbed by the giant squid. Bee appears as the Eight Tails and saves Motoi. When Motoi asks Bee why he saved him despite his attempt to kill him, Bee answers in a rap that it is because they are friends.

Having reached an understanding with Killer Bee, Naruto uses what he learned to overcome his dark self while thanking his counterpart for shaping who he is now. Bee declares himself Naruto's instructor while taking him and Yamato to a temple behind the waterfall, explaining it to be a training ground for Jinchuriki to directly confront and tame their Tailed Beasts. Bee, Yamato, and Naruto enter a chamber where Naruto must fight the Nine Tails once opening his seal, Bee advises the youth to extract the Nine Tails' chakra as Naruto takes advantage of his mediated state to assume Sage Mode.

During his battle with the Nine Tails, Naruto is almost consumed by the tailed beast's hatred when a red-haired woman intervenes. Despite Naruto's assumption that she was illusion, she introduces herself as the chakra imprint of his real mother Kushina Uzumaki. Kushina tells her story about how she met Minato Namikaze in the Academy and how she used to hate her red hair because others made of fun of her. Kushina's views of her hair changed when Minato used it to track down Hidden Cloud ninja who kidnapped her because of her special chakra, falling in love with Minato as a result. She then entrusts Naruto that he will fulfil their dreams.

Naruto manages to defeat the Nine Tails and extract its chakra before imprisoning the monster in a new seal, promising to set things right with the tailed beast. Revealing that Minato gave her time, Kushina decides to give Naruto the full story about the Nine Tails attack on the Hidden Leaf Village. She begins by revealing herself as the previous Nine Tails Jinchuriki from the Hidden Whirlpool Village, a close ally of the Hidden Leaf Village that was destroyed as others feared her people's powerful sealing techniques. Kushina then explains that the seal on the female Jinchuriki wavers during their pregnancy, having been moved to a secret location along with Minato, the Third Hokage's wife, Biwako Sarutobi, a medi-nin named Taji, and an ANBU team. But the ANBU are all killed by Tobi as he infiltrates the venue.

Kushina successfully delivers Naruto, but their celebration comes short when Tobi suddenly appears, killing both Taji and Biwako before holding the newborn hostage to keep the Fourth Hokage from restoring the seal on Kushina. Though Minato quickly saves Naruto, Tobi succeeds in freeing the Nine Tails and placing it under the control of his Sharingan. Kushina survived the extraction, saved by Minato when Tobi orders the Nine Tails to kill her. Minato leaves Kushina with their son as he pursues the masked ninja, who summons the Nine Tails to attack Konoha. As Minato arrives in Konoha and warps away the Nine Tails' Tailed Beast Bomb, Tobi engages Minato in a battle of teleportation until Minato cleverly defeats his opponent with his Rasengan while applying the contract seal to remove control of the Nine Tails.

Kushina's chakra imprint finally departs from Naruto's psyche and Naruto promises himself that he will train hard and surpass the previous Hokage in pursuit of his dream to become the next Hokage. Naruto wakes up and displays his new ability to assume Nine Tails Chakra Mode, his ability to sense negative emotions, allowing him to sense Kisame from Samehada. Revealing that Ay and Bee killed a decoy while he hid himself within Samehada until the time is right while taking Killer Bee's chakra, Kisame escapes with the intent to inform Tobi of the Jinchurikis' location. But he ends up facing Guy, who mistook the Akatsuki member as his reflection, losing Sameheda to Bee despite using his weapon to replenish his chakra while escaping. Guy manages to intercept Kisame as he was about to give a scroll to a shark, defeating the chakra-absorbing villain with his technique Hirudora.

After being defeated by Guy, Kisame is restrained by Yamato so Aoba can gather intel. Aoba peered in Kisame's memory of killing a cipher team per his assignment when their capture by Hidden Leaf Ninja is immediate, later killing his superior to take his place among the Seven Swordsmen while learning the Fourth Mizukage Yagura Karatachi is controlled by an unmasked Tobi. Before Aoba can see Tobi's face, Kisame bit his tongue to regain consciousness and breaks out of his restrains to create a water dome around himself. Having joined the Akatsuki because Tobi promised him a world without lies, remembering Itachi's words of how one finds self-worth at the moment of their death, Kisame allows himself to be devoured by his shark summons. The group is impressed by Kisame's resolution towards his comrade that Guy finally acknowledges Kisame. But when they open the scroll Kisame intended to deliver, they trigger a trap and are contained in water prisons as a summoned shark spirits the scroll away.

Having left the Akatsuki, Konan remembers an event from her past while Jiraiya lived with her, Nagato, and Yahiko. Konan then senses Tobi arriving to the Hidden Rain Village to retrieve Nagato's Rinnegan, having expected him as she takes him to the outskirts while explaining Nagato's resting place is not in the village. While fighting Konan as she denounces him for stealing the Akatsuki from them, still perplexed by why she and Nagato sided with Naruto, Tobi reveals that he influenced Yahiko while claiming that as Madara, he gave Nagato his eyes. Konan refuses to hand Nagato over to Tobi as she transforms into thousands into paper bombs to take the masked ninja out, only for both to survive with the masked ninja's right arm destroyed and his mask partially damaged. Konan responds that she has placed the faith in fallen friends' ideal to Naruto, revealing the sea under them to hold six hundred billion paper bombs.

Konan uses her six hundred billion paper bombs against Tobi to exploit the limits of his teleportation and intangibility jutsu to assure his death, exhausting most her chakra in the process. But Tobi thwarts the gambit by using Izanagi at the cost of his left eye, impaling Konan while explaining the technique's similarities to the Rinnegan through Senju and the Uchiha clans both being descendants of the Sage of Six Paths. Declaring himself as Madara Uchiha, the Second Sage of the Sixth Paths who perfectly assimilated Hashirama's cells, Tobi defeats Konan and while denouncing her faith in Naruto as foolish. Tobi then uses his remaining Sharingan to force her into revealing the location of Nagato and Yahiko's tomb before ending her life. Once obtaining Nagato's corpse, Tobi returns to the Akatsuki's base where he repairs his body and changes into new attire before Zetsu presents Kisame's intel on the jinchurikis' location.

Naruto begins his top secret S-rank mission as an animal surveyor, still unaware that it is actually a distraction to keep him in the dark about the upcoming war while the island itself is revealed to be a giant turtle. Naruto's task to get the animals into a shelter results in him encountering a stowaway Condor and getting caught in a spat among the giant animals smitten over a giant armadillo. At the Akatsuki hideout, Kabuto reveals what he knows of Project Tsuki no Mi and his desire to experiment on Zetsu while convincing Tobi to let him go after the jinchuriki and Yamato. Tobi accepts the proposition, taking Kabuto to a chamber where the Gedo Statue rests on a flower with an unconscious clone of Hashirama Senju's body fused into it. Tobi reveals the flower's roots hold a preserved army of 100,000 White Zetsu, created from the captive tailed beasts' chakra and ready for deployment. When the five Kage learn that the Akatsuki now know the jinchurikis' whereabouts, Onoki offers to travel to the island alongside his bodyguards. Onoki intercepts Kabuto and the reanimated Deidara on the way.

With the giant turtle intercepted by the Manda clone he created from the original, Kabuto has Deidara use a bomb to flip the turtle on its back to immobilize it after they eluded Onoki. Inside the turtle's shell, Yamato, Motoi, and Aoba convince Naruto to continue his animal survey while they investigate. As Onoki and Akatsuchi lure Deidara away from the turtle so the Tsukikage can safely use his Particle Style, the arrival of Yamato's group allows Kurotsuchi's Quicklime jutsu to ensnare Kabuto. But as Aoba attempts to extract information from him, Kabuto reveals to have lulled the group into a false sense of security as he sheds his skin to become a monster that spirits Yamato away into Manda II's nostril before falling back to Deidara's dismay. Tobi, having replaced his left eye with one of Nagato's, is assured of Kabuto's intentions of using Yamato's cells in modifying the White Zetsu.

Onoki transports the giant turtle safely back to the Hidden Cloud Village, while Killer Bee starts training Naruto. At the outskirts of the Akatsuki hideout, Tokuma discovers the White Zetsu Army with his Byakugan and relays the intel to the Five Kage. The Allied Shinobi Forces are then assembled into five battle platoons based on their combat specialty, as well as 3 support platoons: Intelligence, Medical/Logistics and Reconnaissance. Gaara assumes the position of Captain of Battle Squad Four, and Commander in Chief of all five battle units. Meanwhile, Kabuto summons his army of reanimated ninja that include deceased Akatsuki members, previous Kage, the most recent Jinchuriki of the captive tailed beasts, and other powerful ninja. With both the reanimated ninja and a fully-modified White Zetsu Army, Tobi and Kabuto head out to commence the Fourth Great Ninja War.

After he and Tobi mobilize their army, Kabuto captures Anko when she sends her teammates to relay their intel to the Allied Shinobi Forces. Meanwhile at the Hidden Cloud Village, ninjas from different villages started arguing each other until Gaara gives a speech on how Naruto enabled him to discard his hatred and accept him as a friend. Gaara finishes by stating that they all stand as one shinobi to protect Naruto from the Akatsuki. The argument stops, ninjas start forgiving each other and everyone praises Gaara. After the speech, the Allied Shinobi Forces now mobilize towards the enemy.

Kankuro leads the Allied Shinobi Forces' Commando Unit consisting of Sai, Omoi, the Hidden Leaf's Taji, and the Hidden Stone's Ittan into enemy territory and set up a perimeter to locate Kabuto so they can force him into breaking the Reanimation Jutsu. But they are ambushed by a unit overseen by Deidara and Sasori who have captured Anko's subordinates with Muta Abarame being manipulated by the latter as a suicide bomber with Taji wounded attempting to save him as Ittan sinks their outpost to avoid the blast. Tokuma and Ranka descend to attack Kankuro's unit until Omoi feints an attack on Deidara to cut Sasori's chakra strings, saving Tokuma and Ranka while Kankuro pulls Sasori down as Ittan raises their outpost. As Sai joins the fray and recognize his brother Shin with the enemy, Kankuro recalls his last clash with Sasori while meeting the puppet master in his true form before summoning Sasori's puppet body to settle things.

Sasori gloats to have finally gained his ideal immortal body before the battle between the two divisions resumes, Shin revealed to have Deidara's explosion clay inside him as he is manipulated by Sasori to attack. Though Kankuro sacrifices Salamander to encase Shin and contain the blast, Shin's body reconstitutes with Deidara gloating to continually use him as a bomb. Deidara's remark enrages Sai as he knocks him and Sasori out of the air and into Kankuro's awaiting puppets, with Omoi using his lightning style to defuse Deidara's clay. Though Sai expected to fight Shin, his brother instead departs for the afterlife as seeing the finished drawing of both him and Sai holding hands broke the Reanimation jutsu's hold on him. Sasori also departed after being moved by Kankuro's speech of how he obtained immortality through the puppets he created, entrusting the younger ninja with his Mother and Father puppets so they can be passed them down to the next generation. As Kabuto senses the loss of Sasori and Shin, Tobi begins to suspect Kabuto is playing him and the Allied Shinobi against each other.

Killer Bee attempts teaching Naruto to use the Tailed Beast Bomb, Gyuki briefly taking over to explain the risks of Naruto prolonging his Nine Tails Chakra Mode or using clones while in that state. When Naruto learns the Rasengan was modeled after the Tailed Beast Bomb, he undergoes training to figure out the right dosage of yin and chakra to use. Meanwhile, insisting he needs Anko alive to siphon Orochimaru's chakra from her, Kabuto complies with Tobi's insistence to explain the Reanimation Jutsu's workings. Tobi provides Torune and Fu and snaps the former's neck, Kabuto explaining the process while making incapacitated Fu into the vessel for a reanimated Torune. Kabuto adds that he cannot summon the first four Hokage whose souls are currently contained within the Reaper Death Seal, revealing that the jutsu can be undone by its user. Meanwhile, Ao detects a large number of White Zetsu moving underground with Kitsuchi and Kurotsuchi use their Erupt jutsu to flush them out.

Sai, Omoi, and Zaji are grounded by a group of advancing reanimated ninja which Zabuza and Haku are members of, Kakashi's division arriving in time to save them. While the other reanimated ninja are revealed to be the Hiddan Sand's Scorch-Style user Pakura and the Hidden Stone's explosion ninja Gari, Kakashi and Sakura recognize Zabuza and Haku as the former reveals to their former enemies how they influenced Naruto while giving Haku closure of Zabuza's final moments. But Kabuto removes Zabuza's group of their free will as Zabuza and Haku ask Kakashi to stop them, gaining reinforcements in former members of the Seven Ninja Swordsmen of the Mist.

Suigestu explains the Seven Ninja Swordsmen of the Mist to Jugo, mentioning his brother Mangetsu and the group's strongest members who Kabuto had reanimated, Kakashi's group face the swordsmen as Mangetsu summoned their weapons. Gari and Pakura run off while Zabuza uses his mist so the other swordsmen can pick off the ninja. Kakashi forms a plan to remove Zabuza from the fight, but history repeats itself with Haku blocking while Kakashi dodges Zabuza's fully restored Executioner's blade. Remembering how Naruto spoke of them after their mission ended, Kakashi defeats Zabuza so he and Haku can be quickly sealed. Telling Sai that his sealing jutsu is next, a livid Kakashi picks up the Executioner's Blade with the intent to go all out. Meanwhile the Second Division battle the White Zetsu while Gaara's division are about to face their opposition in the form of the reanimated Second Tsuchikage Mu.

Mu proceeds to summon the Kage that Kabuto reanimated, explaining their situation while arguing with Second Mizukage Gengetsu Houzuki over the duel that killed them years ago. They are surveyed by Gaara, who sees the group to include his father: the Fourth Kazekage Rasa. Meanwhile, the Allied Shinobi Forces headquarters learn Darui's coastline division will be facing the White Zetsu and a powerful reanimated ninja group consisting of Kakuzu, Tsunade's former lover Dan Kato, Neji's father Hizashi Hyuga, and the Gold and Silver Brothers Kinkaku and Ginkaku. Ay is dissaded from joining the fight by his strategist Shikaku Nara, who reformulated a battle formation so all divisions can acquire ample support. But Onoki decides to join Gaara's forces to counter the threat Mu presents in being both undetectable and possessing a Kekkei Tota like himself.

Black Zetsu arrives to the fortified palace that the Feudal Lords have gathered at, intending to take them hostage. But Black Zetsu falls back after finding the Lords were fake and maintains his surveillance on the ground. Meanwhile at the coastline, the White Zetsu and the reanimated ninja attack as Hizashi confronts his brother Hiashi while reiterating that his death was for their clan's sake. At the desert, Shikamaru receives orders from headquarters to assist Darui's division while Temari is concerned over their division facing a powerful Kekkei Tota shinobi. While Onoki joins up with the Fourth Division, Darui faces Kinkaku and Ginkaku.

Ay explains to Tsunade that Kinkaku and Ginkaku are two of the Hidden Cloud's most feared criminals, having nearly killed Tobirama when they attacked him during the peace conference with the Second Raikage. Ay also reveals the brothers use items belonging to the Sage of the Six Paths like the Bashosen war fan which utilizes all five Chakra natures, able to endure the items' use from ingesting some of the Nine Tails's chakra. Through Samui and Atsui assist Darui in fighting them, the brothers trap them in the Benihisago gourd through using a combo involving the Kokinjo rope that reveals one's spirit word and the Shichiseiken blade that curses it. Darui manages to change his spirit word when he almost got himself sealed, stealing the brothers' tools and trapping Ginkaku inside the Benihisago. But this provokes Kinkaku into entering his pseudo-Jinchuriki mode.

Kinkaku transforms into a pseudo-Nine-Tails in response to his brother being sealed, overpowering Darui's division. At the headquarters, Ay's handpicked secretary Mabui uses her object teleportation jutsu to transfer the sealing pot known as the Kohaku no Johei to Darui's group as they are joined by Shikakumaru and half of the Fourth Division. Darui manages to seal Kinkaku with Team Asuma's help before Kakuzu arrives and reveals his side's own their gold and silver pieces in the form of Dan Kato and a reanimated Asuma Sarutobi.

As the Surprise Attack Division attempt to retreat to the rendezvous point, they are chased by Akatsuki's reinforcements. Summoning his salamander Ibuse, Hanzō orders it to attack. Unleashing a paralyzing mist of poison, the division is rendered paralyzed and left at Hanzō's mercy. However, Mifune and his division soon arrive and he deflects the would-be devastating blow. Conversing about the past and the paths they had chosen to walk, as the two trade blows, Mifune is able to break Hanzō's sickle and respirator. Remembering his encounter with Mifune in life, Hanzō moves towards his broken kusarigama and using the blade commits seppuku, telling Mifune that he entrusts him with his conviction. This act cuts the poisonous sac that had been in Hanzō's body since he was a child, and causes the poison to leak out and evaporate. Shocking Kabuto Yakushi, Hanzō's body ceases to respond to his orders and the legendary shinobi is soon bound and sealed.

Team Asuma's reunion with their sensei Asuma continues as Choji somewhat loses his will to fight. Ino manages to enter Choji's mind and tells that the meaning of their earrings that Asuma gave to them years ago. After Shikamaru recalling Asuma's last words, he scolded Choji and telling that they are not the ones to be protected but to stand up and protect others. After remembering his promise to be the Akimichi clan's next head and butterfly that started as kind caterpillar, a fully resolved Choji uses his Calorie Control to enter a slimming Butterfly mode. The trio then manage to defeat Asuma, who comments on their perfected Ino-Shika-Cho formation while being sealed.

As Naruto Uzumaki and Bee enter the war, they defeat the White Zetsu Army. Quickly turning the tides of the war, the powerhouse duo make short work of the opposition thanks to Naruto's new ability. Naruto sends several clones to the battle fronts. Naruto and Bee then arrive just to save Musai and Nonata from a reincarnated Toroi, who is promptly sealed. Meanwhile, the Logistical Support and Medical Division's compound is at a standstill with no one allowed to go near the central tent where Shizune and Sakura Haruno were conducting their autopsy. Through research they were able to gather more information which they pass along to HQ. Elsewhere on the Fourth Division's battlefield, the reincarnated Kage draw ever closer to Gaara and Ōnoki's location. Alerted by Mū, that two persons were approaching, the Kage are greeted by an enormous torrent of sand which the Second Mizukage animatedly comments about. Believing it to be the work of Shukaku, the Fourth Kazekage quickly stops the sand using his Gold Dust, causing the Third Raikage to acknowledge him as a Magnet Release kekkei genkai wielder. Shocked to not see the beast before him but actually his son, three of the four Kage are captured by sand arms created by Gaara. Mū who was able to avoid capture, is however soon set upon by Ōnoki using the Particle Style: Atomic Dismantling Jutsu to which the previous Tsuchikage responds in kind, the effects of which leaves a giant crater in the middle of the battlefield. Questioning his son as to where the One-Tail was, as the rest of the Fourth Division lingered a ways back awaiting the signal, Gaara informs his father that he was no longer the jinchūriki he had made him.

As the opposing sides converse, the Fourth Kazekage is shocked to learn that Gaara was no longer the host of the One-Tail, and even more so that he had friends and had become the Kazekage. Intent on testing his son's mettle, the two begin battling while Ōnoki signalled the troops to move in before confronting Mū. As the battle waged on, the Fourth Kazekage is shocked to find himself trapped in Gaara's attack alongside the Second Mizukage and the Third Raikage. Seeing the sand manifest in the form of his late wife after protecting Gaara from one of his attacks, the former Kazekage realizes that Karura had been protecting Gaara his whole life. Remorsefully, the Kazekage tells his son the truth of his mother's love for him and apologized; that all he had done for Gaara was rob him of happiness, now realizing that he had actually been unable to judge the true value of things in the end. Shocked to hear the truth of his mother's love for him and what Yashamaru had been forced to lie to Gaara and say, the young Kazekage breaks down crying. Gaara would later tell his father that while his mother was truly amazing, it was his father who had finally given him medicine to heal his wounded heart. With Gaara forgiving him for his past mistakes, the Fourth smiles on as he is sealed away by his son, entrusting the village, and the future to his son.

As they travel slowly towards an unknown destination, Nagato and Itachi wonder who they were going to be forced to fight before crossing paths with Naruto and Killer Bee. Seeing an opportune moment to capture the Jinchuriki, Kabuto interrupts the reunion to have Itachi attack. As they clash, Itachi learns from Naruto that Sasuke Uchiha knows the truth behind the Uchiha Clan Massacre and asks his opponent not to reveal this information to any one else as Nagato joins the fray. Though puzzled, Nagato was forced to attack and the battle between the four shinobi ensue. Retreating atop Nagato's Giant Drill-Beaked Bird, Itachi activates his Mangekyō Sharingan causing the crow he placed in Naruto to emerge from the shocked youth's mouth. Casting Amaterasu, Itachi incinerates Nagato's summons as well as Nagato himself, revealing that the crow possesses the surgetically embedded eye of Shisui Uchiha, which was rigged to react to Itachi's Mangekyo Sharingan and cast Kotoamatsukami: which had the order "protect Konoha". Now freed from Kabuto's control, Itachi explains that this was the power he had given to Naruto and had intended it for Sasuke. During this explanation, however, Nagato's corpse was able to regenerate. And Kabuto, excited by the prospect of acquiring Shisui's eye, had Nagato attack with his Giant Snake-Tailed Chameleon. Managing to absorb some of Bee's Eight Tails chakra, Nagato is restored to his youthful-looking self as he captures Naruto and prepares to remove his soul.

As Naruto fights to clutch onto his soul that the now-revitalized Nagato was attempting to remove from his body, Bee arrives at their location and attempts a surprise attack but it is foiled by the shared field-of-vision Nagato has with the Giant Snake-Tailed Chameleon and the King of Hell which had been summoned to store the young man's soul. In the clutches of Nagato's mechanical arms with a cannon pointing at him in point-blank range, the two jinchūriki are saved by Itachi and his Susanoo. Nagato, however, quickly regenerates and uses Chibaku Tensei with the intent of crushing his targets into the planetary body. Though Naruto raised the alarm that there was little they could do against this technique, Itachi rallies the group and has them use their most powerful long ranged attacks to target the center of the sphere, effectively neutralizing the attack. In the aftermath of this, Itachi is able to pierce Nagato with his Totsuka Sword freeing the Rinnegan-wielder from Kabuto's control. With the time he had left, Nagato lamented the fact that he had sullied the brilliant legacy their master had left behind and told Naruto to be the most amazing end to the trilogy that he could be. With this, Naruto tries to move out to the battlefield, but his Nine-Tails Chakra Mode wears off leading Itachi to tell him to not rely solely on his own power, but to put some trust in his comrades and their own power. After telling Bee to take care of Naruto, Itachi incinerates the crow with Shisui's Sharingan and departs to deal with the person controlling the reincarnated shinobi.

The Second Mizukage and the Third Raikage manage to escape Gaara's sealing jutsu and battered the shinobi platoon. As the former Kages relay their strengths and weaknesses, the Second Mizukage summons a giant clam that creates a mirage. Gaara leaves the platoon to face Mu and the shinobi platoon had no choice but to fight the Second Mizukage. Onoki and Mu trade blows to each other until Gaara arrives to assist Onoki. Shocked, Gaara sees Naruto delivering Mu with his Planetary Rasengan which Mu quickly evades but with the support of Gaara, Naruto manages to land his new Rasengan jutsu to Mu. Just as Mu to be sealed, Mu utters a warning yet the sealing stops his talking. Meanwhile, the Second Mizukage argues with the platoon that they should not attack what they see him and the clam. Gaara arrives and manages to sense the location of the giant clam and Onoki delivers a powerful Earth style punch despite running low on chakra. However Onoki gets exhausted and the Second Mizukage appears on his behind with the index finger pointing at Onoki's back. The Second Mizukage shoots Onoki with a water gun jutsu developed by the Hozuki clan.

As the Fourth Division's attacks prove futile against the Third Raikage, he re-emphasizes how they were to attack him. Temari and a few other tessenjutsu users attack the Third with the Wind Release: Cast Net technique which appears to have finally incapacitated the Raikage, but as shinobi from the Sealing Team move in to bind him, they are sent reeling. Spotting his former aide Dodai amongst the Allied Shinobi Forces' ranks, he steps forward and tells Temari a bit more about the Raikage and noted that they needed a more powerful Wind Release technique to attack him. Noting that there was not a more powerful Wind Release user amongst their ranks or even in the Alliance, Naruto's shadow clone arrives, announcing that he would be able to do the job. Leaping into action, Naruto forms a Rasenshuriken which after some manipulation, finally lands an attack on the Raikage which proves to be just as futile. Retreating as the Third's persona, Dodai instructed the Earth Release users to erect a wall which he himself fortifies. Telling his comrades to retreat nonetheless, his words fall on deaf ears as the Raikage breaks through the wall using his Hell Stab. As the division is set upon again, Naruto and Dodai discuss the legacy of the Raikage leading Naruto to want to know how the Third got the scar on his body which was noted to be the "ultimate shield". Needing to ask the Eight-Tails directly, Dodai creates a distraction which the Third chases, buying them time to contact Inoichi Yamanaka who patches them through to Bee. Upon hearing of the monstrous battle between the Third and the Eight-Tails, Naruto formulates a strategy using Sage Mode as his cloak had dissipated due to attempting to make a Tailed Beast Ball. Ultimately, the Third ends up stabbing himself with his One-Finger Nukite, and his body begins to disintegrate and he is eventually bound and sealed. Dodai surmises that in the end, no one person could have the strongest shield and spear, noting that in the end, the Third had the strongest spear. Naruto agrees, noting that Gaara of the Sand probably had the strongest shield. Meanwhile on Gaara's battlefield, the division struggle to defeat the Second Mizukage.

Ōnoki is revealed to be a sand clone shocking the Second Mizukage as the sand rose up to seal him. However, before the tags can be completely applied, Gaara's Desert Layered Imperial Funeral explodes and the Mizukage's ominous face appears in the sky above them. As hail begins to fall, Ōnoki explains that this was not genjutsu again, but the Second's Steaming Danger Tyranny technique. As a chibi-like clone forms before them and begins to attack the Fourth Division, Gaara sets out to find the real Mizukage who, as the Tsuchikage noted, had been left severely weakened after using this technique. Finding him, Gaara moves to immediately seal the Mizukage, but once again before the seals can be applied, the clones intervenes this time, ripping them off the sand pyramid. Popping his head out from atop the pyramid, the Second greets his opponents serenely before ducking back in to avoid a volley of shuriken launched at him. Commenting that this was a good spot to hide, the Mizukage tells the Kazekage and Tsuchikage that he would no longer divulge the mechanisms behind his techniques, because if they were unable to defeat him, they had no hope of taking on the opposition's leader. Narrowly protecting his division from another explosion, Gaara then directly takes on the clone and is successfully able to stop the clone after using a mixture of his sand drenched in hail and his father's gold dust to both halt the clones movements and stop it from exploding by keeping it cool. Greatly impressed by this feat, the Second beams at Gaara stating that he and Naruto who had made his way to the battlefield eventually made a good combination. Before being sealed, the Second declares that he had found the golden egg amongst the current Kage after all. Elsewhere on the battlefield, it is revealed that before being sealed away, Mū had split himself in half. Unable to free his other half, Kabuto contemplates his next move which would buy him enough time to summon his trump card. On the Alliance's side, everything has come to a standstill in the face of the threat of the White Zetsu Army clones infiltrating their ranks, especially at the Logistical Support and Medical Division.

The White Zetsu Army continues wreaking havoc on the battlefields with the Allied Shinobi Forces struggling to root out the impostors until Naruto Uzumaki arrives, dispersing his shadow clones and use his sage Jutsu to weed out the White Zetsu with the Allied Shinobi regaining the upper hand. As reports come into HQ of Naruto's part in turning the tides of the war back in their favor, Tsunade smugly gestures to A who solemnly dismisses her. The Sensor Division is asked to check on Tobi’s status and Ao revealing that he is on move with a team of reincarnated jinchūriki. Meanwhile where the remainder of the Fourth Division is located, Kabuto puts his trump card into play as he uses Mū to summon the coffin holding it. After Mū dodges the coffin being blown off, a sensor amongst the Alliance alerts them to a new enemy. Ōnoki recognizes the figure to be Madara Uchiha himself. Believing their enemy to have finally entered the fray, Gaara's revelation that Madara is a reanimated ninja causes confusion as Temari reveals the masked man who called himself Madara is seen elsewhere with a personal army of reanimated Jinchuriki.

Though believing he was resurrected, Madara learns he was brought back with the Reanimation jutsu instead as Kabuto takes control over Mū's body to explains that he deduced the truth and reanimated Madara to force Tobi into their alliance. Madara is also informed of the modifications Kabuto done of his body and the events that occurred after his death before he proceeds to take down a large portion of the Fourth Division with his Susanoo. Madara then reveals that he possesses the Rinnegan when Gaara, Onoki and Naruto attack him, confirming Kabuto's hypothesis that Madara acquired a sample of Hashirama’s blood when he faked his death in the events that created the Valley of the End. Madara then wipes out a fraction of the Fourth Division with his Shattered Heaven attack despite Onoki stopping one of the two summoned meteorites, attempting to summon the Nine-Tails before learning that the tailed beast is sealed within Naruto. Madara then proceeds to reveal that he possesses Hashirama's cells by using the First Hokage's Secret Wood Style Jutsu: Deep Forest Emergence, leaving Naruto and the other surviving shinobi of the Fourth Division in shock.

As Onoki and the remaining Fourth Division members tackle both Madara and Mū, Tsunade and A take a risky gambit to reach Madara's through Mabui's Heavenly Transfer Jutsu, normally used for transferring objects. Despite the high probability of being killed by the Jutsu, Tsunade decides to take the gamble using her Reverse Seal: Release. Shikaku telepathically communicates to Genma to have him, Raidō and Iwashi perform the Flying Raijin Justu to transport Mei to Madara's location as well while Naruto distracted Black Zetsu long enough for Chojuro to defeat the inhuman being. When the other Kage arrive at the battlefield, Tsunade heals Gaara and Onoki while A and Mei engage Madara as Dodai and the Hokage Guard Platoon chase after the Kabuto-controlled Mū. Once healed, the two saving A and Mei from their enemy's Yasaka Magatama, Gaara holds Madara at bay while Onoki joins the Kage under the cover of Mei's Hiding in Mist Jutsu to use a jutsu that effects A's weight so he can knock Mū and Madara a distance away. Though Naruto wants to help, Tsunade tells the boy that they will deal with Madara while he goes after the "other Madara". As the clone disperses, the Kage leave him one word: "win". At the same time, Naruto and Killer Bee cross paths with Tobi and the reanimated Jinchuriki.

Acquiring the knowledge from a clone fighting the real Madara while head butting Tobi, Naruto battles reanimated Jinchuriki while recognizing Utakata and meets him in a metaphysical plain. Utakata reveals what became of him after he left Tsuchigumo village and was captured by Pain before Naruto returns to reality as he and Bee battle the reanimated Jinchūriki. Naruto mentions meeting the real Madara with Tobi proclaiming his true identity is pointless as only the Project Tsuki no Mi matters to him, Tobi explains the world is worthless and that both Naruto and Bee should understand the misery it holds better than anyone else. However, Naruto admits his life with a Tailed Beast inside him isn't that bad while calling Tobi a liar and vowing to unmask him. As each of the reanimated Jinchuriki grows a tail, Tobi declares he will capture Naruto and Bee to fulfill his plan.

After he and Naruto learn that the captive Tailed Beasts have been resealed into their Jinchuriki, Killer Bee makes the first move by attacking Fu but he and Naruto learn the reanimated Jinchuriki are able to use the coordination of the Rinnegan's Six Paths of Pain in conjunction with the Sharingan's increased reaction time. Naruto attempts to destroy the Chakra receivers while Bee transforms into Gyuki to level the forest while knocking down the other Jinchuriki. But the reanimated Jinchuriki strike back with Han transforming into the Five-Tails while the others attack Naruto. Though Tobi attempts to use Kamui on Naruto to increase the odds in his favor, his plot is foiled by Kakashi Hatake and Guy arriving in the nick of time. Though Tobi tells them that they still have no chance against his eyes and Tailed Beasts, Kakashi states his Sharingan while Guy adds his notability as Konoha's Sublime Green Beast of Prey.

After killing White Zetsu with his Eternal Mangekyo Sharingan's Susano'o, Sasuke Uchiha sets off to destroy Konoha. Back at the battlefield, as Kakashi and Guy learn that Tobi is using a large amount of chakra to assert full control over the Tailed Beasts, they hear the voice of the Five Tails as Tobi subjugates the creature. Voicing his disdain for humans' treatment of them, the Nine Tails recaps his own subjugation under Madara and then by the Uzumaki Clan from Hashirama's wife Mito to Naruto's mother Kushina. After Roshi fully transforms into the Four Tails, he swallows Naruto. The Four Tails meets Naruto and insists that he be called by his actual name: Son Goku. After a brief discussion about the humans' treatment of the Tailed Beasts, during which Naruto learns the Nine-Tailed Fox's true name is Kurama, Son sees Naruto to be an exception. Wanting to know if Naruto's desire to aid him and the other Tailed Beasts would not waver, Son asks the youth to free him from his chains.

Before revealing the method by which to stop him, Son verbally states his distrust of Naruto from his past experience with Jinchuriki. As Kurama listens to their dialogue, he relates to Son's distrust since he was also simply used and sealed by many ninja in the past. Losing himself in thought, Kurama recalls the events of how he ended up in Naruto’s body and of the numerous attempts he made to break free by weakening Minato's Eight-Trigram seal and influencing Naruto with his own chakra on many occasions. But following a series of trials and battles, Naruto frees himself from his own hatred with Killer Bee's help and successfully takes control of the Nine-Tails chakra, leaving Kurama to ponder just what type of person Naruto actually is.

Though Son Goku awards him with a fragment of his Charka for freeing the Tailed Beast from Tobi’s control, Naruto is upset upon learning Son keep hidden that he would still be bond to the Gedo Statue. Once Son is sealed back into the Gedo Statue, Tobi has all the other Jinchūriki fully transform into their Tailed Beasts for an all out attack. Silently proud of Naruto winning Son over, Kurama offers to lend the youth more power. Though annoyed of being thanked for helping Naruto during his clone’s encounter with Madara, Kurama suggests melding their chakra together. Declaring Kurama as a friend while removing the seal, their blended chakra enables Naruto to assume a stronger version of his Nine Tails Chakra Mode. In his new Tailed Beast Mode, saving Kakashi and Guy, Naruto uses his remaining time in the form to battle the five Tailed Beasts while his clone locates their chakra receivers. The five Tailed Beasts make a collaborative Tailed Beast Ball, which Naruto matches with one of his own, sending the attacks into the sky. He sends clones through Kurama's chakra arms to remove the chakra receivers. Upon touching them, Naruto finds himself in a mental plane, along with Kurama, the other Jinchuriki and their Tailed Beasts. After the Jinchuriki and the Tailed Beasts give Naruto their names, they reveal the relationship between Roshi and Son to the youth. Watching his fellow Tailed Beasts each gift Naruto with a bit of their chakra like Son had, Kurama recalls their last moments with the Sage of the Six Paths at the time of their creation long ago. As Naruto removes the chakra receivers, Kurama is assured by the others' agreement with him that Naruto is the one the Sage foretold to show them the way. Forced to seal the Tailed Beasts back into the Gedo Statue, Tobi tells a reverted Naruto that his victory changes nothing despite the youth insisting that it has after learning a lot of difficult names.

Tobi is confused by Naruto's claim of learning difficult names, which Naruto teases him for. Guy and Kakashi discuss now Naruto's progress is making them feel old, though not that old. Tobi begins to sweat, but assumes be the starting rainfall. Tobi gets a strange feeling from Naruto, and concludes that the war will make everything irrelevant. At the Allied Shinobi's HQ, Naruto's use of Kurama's chakra was felt, though they also feel something else. Ao relays the events to Shikaku, who wants to use it to raise the army's morale all at once, despite the strain it would cause to communications by Inoichi. Naruto's friends all rush towards his direction, intent on supporting him. Elsewhere, Sasuke also walks towards the battlefield as a thunderstorm begins.

The Ten-Tails fires its enormous Tailed Beast Ball at the Alliance. Shikamaru, with the help of Ino's jutsu, devises a last-minute plan to counter its powerful attack by creating an earth barrier and Bee slowing down the Tailed Beast Ball, changing its trajectory. However, the attack manages to pierce through the barriers of the Alliance and Bee quickly blocks it on his own. The ball suddenly disappears as Minato arrives, telling the Alliance that he teleported it to the sea. The other Hokages soon arrive and create a special barrier to trap the Ten-Tails. Sasuke arrives, much to the shock of Konoha 11, and he tells them that he has decided to protect the village and aspires to become Hokage. Reuniting with Naruto and Sakura Haruno, Team 7 prepare themselves against the Ten Tails. Meanwhile in Kamui's dimension, Obito continues to berate Kakashi about the failing reality in this world and value of comrades but Kakashi tells Obito that losing the feelings of his comrades is much worse than trash and he believes that his comrades will fill the hole inside his heart.

The wedding is a week away. Iruka thinks about Naruto from his childhood and how he still hasn't given his message for the wedding. After class, he talks with Hinata, who says everything is ready. While cooking dinner, Iruka is visited by Naruto, who asks Iruka to attend as his father. Iruka happily agrees and realizes that Naruto also doesn't see their relationship as teacher and student but as family. Iruka gives his message, warning Hinata of Naruto's immature tendencies and stating that Naruto better make her happy. On the day of the wedding, everyone attending gives packets of money as the five Kage arrive. Shikamaru and Temari, as well as Ino and Sai, attend as couples. Sakura receives a congratulations letter from Sasuke's hawk and the two think about each other while he continues traveling. Naruto looks at Minato's headstone as Hinata thinks about Neji. Hiashi and Hanabi come in to tell them it is time. Naruto and Hinata then begin walking to the ceremony to get married.